I want to publish more and read less

I need to publish more and read less

Cameron Neylon - Munin ConferenceTromsø - 22 November 2011

Wednesday, 14 December 11

http://www.flickr.com/photos/cappellmeister/39508741 CC-BY

technologies...

conceptual changes...

http://www.flickr.com/photos/ivanwalsh/4509575889 CC-BYWednesday, 14 December 11

...central principle.

http://www.flickr.com/photos/mkumm/2709555496 CC-BY

But first.

Helen BermanLorie LeJeune

Iain Emsley

Neil Saunders

Brian Kelly

Harry Collins

Michael Nielsen

Jen Dodd

Greg Wilson

Timo Hannay

Maxine Clarke

Jenny RohnRicardo Vidal Paulo Nuin

Jenny HalePeter Murray-Rust

Deepak Singh

Jon Udell

Tim O’Reilly

David Crotty

Rafael Sidi

Richard Akerman

Jean-Claude Bradley

Mike Ellis

Liz Lyons

Andy Powell

Gavin Baker Peter Suber

Victor Henning

Sabine HossenfelderFlickr

Google

Steve Wilson

Andrew Milsted

Frank Norman

Dave de RoureJeremy Frey

John Cumbers

Bill Flanagan

ISIS LSS Group

Lakshmi Shastry

Catherine Jones

ISIS Computing GroupSTFC

Plausible AccuracyJohn

Dupuis

Chad Orzel

Ken Shankland

Martyn Bull

Jonathan Gray

Rufus Pollock

Clay Shirky

Kevin Kelly

Gavin Bell

Shirley Wu

Euan Adie

Richard Curry Ian Mulvany

Jamie McQuay

Atilla Csordas

Pawel Szcsesny Gabriel Cavalli

Matt Wood

TIM HUBBARD

DUNCAN HULL

Richard Grant Branwen Hide

Friendfeed

Bora Zivkovic

Peter Binfield

John Wilbanks

Kaitlin ThaneyThe BioGang

Tony WilliamsEgon Willighagen

Martin FennerYaroslav Nikolaev

Jon EisenMichael Eisen

Richard Akerman

Jeremiah FaithMichael Barton

Lee Smolin

Garret Lisi

Victoria Stodden

Simon ColesTony Hey

Noel Gorelick

Jon Tansley

Benjamin Good Dorothea Salo

Paul Walk

Mitch Waldrop

Björn Brembs

Rich Apodaca

Bill Hooker

Pedro Beltrao

Mat Todd

SciFoo 2008/9

campers

Stephen Brenner

Brian Matthews

Allyson Lister

Phil Lord

Steve Koch

Koch Lab

Carole Goble

Stephen FriendEva Amsen

JOHN WILLINSKY

TIM HUBBARDTIM HUBBARDTIM HUBBARD

Steph Hannon

Rebecca Goulding

Leigh Dodds

Paul Miller

Mark BorkumDan Hagon

Jim Downing

Nico Adams

@gnatFabiana Kubke

Hope LemanLisa Green

Ariel Waldmann

@tGrace Baynes

Simon Philips

Matt Johnson

Lee Dirks

Microsoft

NPG Ben Goldacre

Arfon Smith

Nicholas Cole

Chris Leonard

PIERRE LINDENBAUM

ALAN CANN

Jo Badge

Mummi Thorissson

Andrew Kasarskis

Glyn Moody

@communicating

PT Sefton

Andrew Farke

Who am I?

http://www.flickr.com/photos/andypowe11/3915450391

I live in Bath

I work at RAL

Wikimedia Commons Succinate_Dehydrogenase_1YQ3_and_Membrane.png

Wikimedia CommonsMGMT BDNA_1T38.png

I work on...

http://www.flickr.com/photos/59937401@N07/5929622407 CC-BY

I write grants...

http://flickr.com/photos/nicmcphee/2756494307/ CC-BY

...and papers...

Slideshare - http://slideshare.net/CameronNeylon/presentations

39 Presentations~100,000 views

http://cameronneylon.net

Papers are not enough...

...software...

...data...

Need to communicate...

http://www.flickr.com/photos/jurvetson/3184362622 CC-BY

all the pieces...

Need to maximise “impact”...

http://www.flickr.com/photos/babasteve/3140688308 CC-BYWednesday, 14 December 11

But that’s ok...

We have new tools...

http://www.flickr.com/photos/kylemay/1430449350 CC-BY

Many new ways and places to publish...

group, and finally attachment to the solid support. In addition theuse of intein based methods as well as the preparation of the solidsupport for Staudinger ligation often require reagents such asphosphines or thiophenols that are toxic and difficult to handle.Therefore there remains a significant need for robust and simple

methodologies for protein immobilization that can be applied towide range of proteins and solid supports. The identification of theSortase transpeptidase [19] provided an alternative approach toprotein ligation. Sortases recognise a specific peptide sequence(LPETG for SrtA of S. aureus used in this work) in proteins targetedfor covalent attachment to the cell wall peptidoglycan. The peptidetag sequence is cleaved and then ligated to the pentaglycine moietyon the peptidoglycan precursor Lipid II. Proteins expressed with theC-terminal recognition sequence can be covalently attached to a widerange of constructs with an N-terminal glycine amidemotif includingpeptides [20], PNA [21], full length proteins [22] and small moleculesubstrates [23]. Another group has independently described anexample of Sortase mediated ligation to a beaded solid support [22].These reactions proceed under aqueous conditions without theaddition of any further reagents beyond the protein, ligationsubstrate, and Sortase. Thus Sortase has the potential to providea means of linking expressed proteins to a wide range of solidsupports which is mild, selective, and can be carried out in a singlestep. Here we investigate the ability of S. aureus SrtA to ligate proteinsto a range of solid supports.

RESULTSPlasmid vectors were constructed for the expression of Bluefluorescent protein (BFP, Q-Biogene), Enhanced Green Fluores-cent Protein (EGFP), a red fluorescent protein (DsRed), and thesequence specific DNA binding protein Tus [24] with a C-terminal LPETGG sequence followed by a hexahistidine tag. Theproteins were expressed in BL21(DE3) and purified beforeattachment to solid supports.Our first target was the immobilization of proteins onto cross-

linked polymer beads. Glycidyl methacrylate (GMA) beads weremodified with a spacer followed by one, two, or four glycineresidues. Mono-glycine, di-glycine, and tetra-glycine beads wereincubated with EGFP-LPETGG-His6 (85 mM) and His6-Sortase A(40 nM) in Sortase buffer (50 mM Tris-HCl, 150 mM NaCl,5 mM CaCl2, pH 7.5). As a control, beads with no glycinecoupled were incubated with Sortase and EGFP-LPETGG-His6,and tetraglycine beads were incubated with EGFP-LPETGG-His6in the absence of Sortase. Samples were taken at various timepoints and beads analysed by FACS (Figure 1) and fluorescencemicroscopy (Figure 2). The labeled beads were clearly visible byfluorescence microscopy while beads from control reactionsshowed no increase in fluorescence. Tetra-glycine beads showedthe most rapid fluorescence increase and the highest finalfluorescence. Di-glycine beads were nearly as effective as tetra-glycine with mono-glycine beads showing slower increase andsignificantly reduced final fluorescence.EGFP and the other fluorescent proteins are extremely robust.

While the fluorescence analysis of the ligation of these proteinsdemonstrates maintenance of function it is therefore of interest todemonstrate that more fragile proteins can be ligated to solidsupports while maintaining function. This is crucial for applica-tions in supported catalysis or bead-based protein arrays. Todemonstrate that ligated protein was functional and accessible toother molecules in solution Tus-LPETGG-His6 was immobilizedon tetraglycine GMA beads. Tus is a sequence specific DNA-binding protein that recognizes 21 bp Ter sites [24]. The Tus-labeled GMA beads were incubated with different proportions offluorescein labeled TerB DNA and a 21 bp Cy5-labeled DNA

sequence unrelated to TerB in binding buffer (50 mM Tris-HCl,250 mM KCl, 0.1 mM EDTA, 0.1 mM DTT, pH 9). The totalDNA concentration (Ter plus nonspecific DNA) was 100 nM forall samples. The fluorescein and Cy5 fluorescence of the beads wasdetermined by FACS analysis. Non-specific DNA binding wasvery low in all cases, consistent with the low affinity of Tus for non-specific DNA in 250 mM KCl [25]. Ter binding showeda concentration dependence that was consistent with anequilibrium dissociation constant of 2968 nM (Figure 3), whichcompares well with values of KD measured by fluorescenceanisotropy (,15 nM at 37uC) or Biacore (,1 nM at 25uC) [25].To demonstrate attachment to other solid supports a beaded

agarose affinity support (Affi-Gel 102 resin, Bio-Rad) was modifiedwith oligoglycine by incubating the amino-resin with diglycine(0.5 M) and EDC (2.5 mM) for three hours at 50uC. BFP-, EGFP-,and DsRed-LPETGG-His6 were then ligated to the resinovernight at room temperature. After washing the resin columnscould be seen to be clearly labeled with fluorescent protein(Figure 4a,b) whereas a control (EGFP without Sortase) showed nofluorescence. The labeled Affi-Gel beads were clearly visible byfluorescence microscopy (Figure 2).

Figure 1. Ligation of fluorescent proteins to polymer beads. (a) GMAbeads modified with one, two, or four glycine residues were incubatedwith EGFP-LPETGG-His6 and Sortase. Samples were taken at specifictime points and analyzed on a BD FACSAria. Controls contained beadswith no glycine or diglycine beads without Sortase. Error bars showingthe standard error in the mean fluorescence are omitted as they aregenerally smaller than the data symbols. Errors are given inSupplementary Data S2.doi:10.1371/journal.pone.0001164.g001

Figure 2. Fluorescence micrographs of labeled solid supports. (a)Diglycine GMA beads and (b) oligoglycine modified Affigel resin wereseparately labeled with EGFP and DsRed and then mixed. Fluorescenceimages were recorded as separate gray scale images (see Supplemen-tary Figure S2) with FITC and Cy3 filter sets and then combined andfalse coloured.doi:10.1371/journal.pone.0001164.g002

Sortase-Mediated Ligation

PLoS ONE | www.plosone.org 2 November 2007 | Issue 11 | e1164

...when we publish...Wednesday, 14 December 11

...publish the data...

...in the right places...

...the software...Wednesday, 14 December 11

...and all the rest?Wednesday, 14 December 11

Flickr tag: UC207

http://usefulchem.wikispaces.com/Exp207

http://www.flickr.com/photos/stuartpilbrow/3345896050 CC-BY-SAWednesday, 14 December 11

This is not sustainable...

“I need to publish more”

...not work more...

We have...

http://www.flickr.com/photos/schnurrbart/43568532 CC-BY-SA

A resource problem...

http://www.flickr.com/photos/mukumbura/4052671706 CC-BY-SAWednesday, 14 December 11

Whether it’s money...

...or time...

http://www.flickr.com/photos/robbie73/3387189144 CC-BY-SAWednesday, 14 December 11

Technical capacity is not enough

...either need to resource it

...or make it cheaper.

Publication as a side effect of recording....

“Publish@Source”Jeremy Frey,Southampton

http://usefulchem.wikispaces.com/Exp258Wednesday, 14 December 11

http://www.carlboettiger.info/Wednesday, 14 December 11

http://www.myexperiment.org/workflows/204.htmlWednesday, 14 December 11

http://www.flickr.com/photos/psychemedia/Wednesday, 14 December 11

Easy to publish pieces...

http://www.flickr.com/photos/horiavarlan/4514164700 CC-BYWednesday, 14 December 11

...and then collect

So we capture and collect...

http://www.flickr.com/photos/furtwangl/3851841424

...then tell the story

Dionaea muscipula Musca domesticachomped on

http://www.flickr.com/photos/lizadaly/2944376209 CC-BY

...aggregate existing pieces

http://www.flickr.com/photos/bladeflyer/442496389 CC-BY

...we can open the floodgates...

...all the way...http://www.flickr.com/photos/fraz5356/4754482759 CC-BYWednesday, 14 December 11

It’ll be great...right?http://www.flickr.com/photos/62337512@N00/3958637561 CC-BY

group, and finally attachment to the solid support. In addition theuse of intein based methods as well as the preparation of the solidsupport for Staudinger ligation often require reagents such asphosphines or thiophenols that are toxic and difficult to handle.Therefore there remains a significant need for robust and simple

methodologies for protein immobilization that can be applied towide range of proteins and solid supports. The identification of theSortase transpeptidase [19] provided an alternative approach toprotein ligation. Sortases recognise a specific peptide sequence(LPETG for SrtA of S. aureus used in this work) in proteins targetedfor covalent attachment to the cell wall peptidoglycan. The peptidetag sequence is cleaved and then ligated to the pentaglycine moietyon the peptidoglycan precursor Lipid II. Proteins expressed with theC-terminal recognition sequence can be covalently attached to a widerange of constructs with an N-terminal glycine amidemotif includingpeptides [20], PNA [21], full length proteins [22] and small moleculesubstrates [23]. Another group has independently described anexample of Sortase mediated ligation to a beaded solid support [22].These reactions proceed under aqueous conditions without theaddition of any further reagents beyond the protein, ligationsubstrate, and Sortase. Thus Sortase has the potential to providea means of linking expressed proteins to a wide range of solidsupports which is mild, selective, and can be carried out in a singlestep. Here we investigate the ability of S. aureus SrtA to ligate proteinsto a range of solid supports.

Figure 1. Ligation of fluorescent proteins to polymer beads. (a) GMAbeads modified with one, two, or four glycine residues were incubatedwith EGFP-LPETGG-His6 and Sortase. Samples were taken at specifictime points and analyzed on a BD FACSAria. Controls contained beadswith no glycine or diglycine beads without Sortase. Error bars showingthe standard error in the mean fluorescence are omitted as they aregenerally smaller than the data symbols. Errors are given inSupplementary Data S2.doi:10.1371/journal.pone.0001164.g001

All of this information...data....

Flickr tag: UC207

http://usefulchem.wikispaces.com/Exp207

http://www.flickr.com/photos/waltstoneburner/3372746317 CC-BY

Retractions per 100k papers30

201020001990198019701960Year

http://www.flickr.com/photos/oakleyoriginals/2879794262 CC-BYWednesday, 14 December 11

watercannon?

http://www.flickr.com/photos/7827294@N04/4621721577 CC-BYWednesday, 14 December 11

Information overload...

http://www.flickr.com/photos/dylanroscover/3450505729 CC-BY-SA

“I need to read less”

Filter failure?

http://www.flickr.com/photos/daveyll/332723930Wednesday, 14 December 11

http://www.flickr.com/photos/biscuitsmlp/2247299538 CC-BY

Filters block.

http://www.flickr.com/photos/emperley3/4705354106 CC-BY-SAWednesday, 14 December 11

http://www.flickr.com/photos/robmcm/1671702203 CC-BY-SA

You think this is a good thing...

http://www.flickr.com/photos/mrehan00/3700858676 CC-BY-SA

...we’re “protecting our community from a deluge”

...staying on the straight and narrow...

http://www.flickr.com/photos/quinnanya/4813974125 CC-BYWednesday, 14 December 11

Or are we just limiting our ability to explore...?

http://www.flickr.com/photos/jurvetson/2174000357 CC-BYWednesday, 14 December 11

http://www.flickr.com/photos/joiseyshowaa/2374526016 CC-BY

...and discover...?

Filters block.

The right filter for me? Right filter for now?

http://www.flickr.com/photos/lotzman/3595748169 CC-BYWednesday, 14 December 11

Remember this graph?30

201020001990198019701960Year

Where is the data from?Wednesday, 14 December 11

201020001990198019701960Year

https://github.com/neilfws/PubMed/blob/master/data/retractions.txt

201020001990198019701960Year

https://github.com/neilfws/PubMed/blob/master/data/retractions.txt

But how did I discover it?

http://friendfeed.com/gbilder/711e6278/so-how-many-retractions-are-there-every-year

Remember these people?

Helen BermanLorie LeJeune

Iain Emsley

Neil Saunders

Brian Kelly

Harry Collins

Michael Nielsen

Jen Dodd

Greg Wilson

Timo Hannay

Maxine Clarke

Jenny RohnRicardo Vidal Paulo Nuin

Jenny HalePeter Murray-Rust

Deepak Singh

Jon Udell

Tim O’Reilly

David Crotty

Rafael Sidi

Richard Akerman

Jean-Claude Bradley

Mike Ellis

Liz Lyons

Andy Powell

Gavin Baker Peter Suber

Victor Henning

Sabine HossenfelderFlickr

Google

Steve Wilson

Andrew Milsted

Frank Norman

Dave de RoureJeremy Frey

John Cumbers

Bill Flanagan

ISIS LSS Group

Lakshmi Shastry

Catherine Jones

ISIS Computing GroupSTFC

Plausible AccuracyJohn

Dupuis

Chad Orzel

Ken Shankland

Martyn Bull

Jonathan Gray

Rufus Pollock

Clay Shirky

Kevin Kelly

Gavin Bell

Shirley Wu

Euan Adie

Richard Curry Ian Mulvany

Jamie McQuay

Atilla Csordas

Pawel Szcsesny Gabriel Cavalli

Matt Wood

TIM HUBBARD

DUNCAN HULL

Richard Grant Branwen Hide

Friendfeed

Bora Zivkovic

Peter Binfield

John Wilbanks

Kaitlin ThaneyThe BioGang

Tony WilliamsEgon Willighagen

Martin FennerYaroslav Nikolaev

Jon EisenMichael Eisen

Richard Akerman

Jeremiah FaithMichael Barton

Lee Smolin

Garret Lisi

Victoria Stodden

Simon ColesTony Hey

Noel Gorelick

Jon Tansley

Benjamin Good Dorothea Salo

Paul Walk

Mitch Waldrop

Björn Brembs

Rich Apodaca

Bill Hooker

Pedro Beltrao

Mat Todd

SciFoo 2008/9

campers

Stephen Brenner

Brian Matthews

Allyson Lister

Phil Lord

Steve Koch

Koch Lab

Carole Goble

Stephen FriendEva Amsen

JOHN WILLINSKY

TIM HUBBARDTIM HUBBARDTIM HUBBARD

Steph Hannon

Rebecca Goulding

Leigh Dodds

Paul Miller

Mark BorkumDan Hagon

Jim Downing

Nico Adams

@gnatFabiana Kubke

Hope LemanLisa Green

Ariel Waldmann

@tGrace Baynes

Simon Philips

Matt Johnson

Lee Dirks

Microsoft

NPG Ben Goldacre

Arfon Smith

Nicholas Cole

Chris Leonard

PIERRE LINDENBAUM

ALAN CANN

Jo Badge

Mummi Thorissson

Andrew Kasarskis

Glyn Moody

@communicating

PT Sefton

Andrew Farke

Social aggregation...

...but also...

Social annotation

...and quality assessment

http://www.flickr.com/photos/pinksherbet/3209939998 CC-BYWednesday, 14 December 11

...but also...

http://nsaunders.wordpress.com/2010/11/30/analysis-of-retractions-in-pubmed/

A network of linked objects...

...primed for discovery...

It’s not filter failure

...it’s a discovery deficit...

http://www.flickr.com/photos/nationallibrarynz_commons/4078337883 Public Domain

http://flickr.com/photos/stewart/461099066/

In the last year...?

...in the past 24 hours?Wednesday, 14 December 11

Is search the answer?

http://www.flickr.com/photos/ezioman/2096469724 CC-BY

http://www.flickr.com/photos/mangostrawberry/5490992826 CC-BY

...or something more...?

Need the right instrument...

http://www.flickr.com/photos/conskeptical/269403030 CC-BY-SAWednesday, 14 December 11

...not every problem is a nailhttp://www.flickr.com/photos/bb_matt/207102083 CC-BYWednesday, 14 December 11

Blog/Wiki!LIMS!

Data repository!Local file stores!

Online file stores!

Map Reduce/!Hadoop!

Workflows!

http://www.flickr.com/photos/striatic/125614 CC-BY

Some way away yet...

http://www.flickr.com/photos/cappellmeister/39508741 CC-BY

technologies...

PublicationAggregationDiscovery

conceptual changes...

http://www.flickr.com/photos/ivanwalsh/4509575889 CC-BYWednesday, 14 December 11

Publish pieces...then aggregate

Don’t filter...enable discovery

...central principle.

http://www.flickr.com/photos/mkumm/2709555496 CC-BY

Networks scale

1982 1986 1990 1994 1998 2002 2006

Average Capacity of Human Researcher

1982 1986 1990 1994 1998 2002 2006

Average Capacity of Norwegian Researcher

People don’t scale...

Neither do computers...

http://www.flickr.com/photos/argonne/3323018571 CC-BY-SA

...at least not on their own

Open networks scale

...closed networks do not.http://www.flickr.com/photos/andypowe11/3759152528Wednesday, 14 December 11

We need...

http://flickr.com/photos/virtualsugar/316200555/ CC-BYWednesday, 14 December 11

Open data...

http://www.flickr.com/photos/jwyg/4528443760/ CC-BY-SAWednesday, 14 December 11

...but also...

...open platforms for innovation

http://www.flickr.com/photos/37984062@N03/3495256118 CC-BY-SAWednesday, 14 December 11

http://www.flickr.com/photos/tomarthur/3593729997

Optimise for....

....not this

http://www.flickr.com/photos/vrogy/514733529

http://www.flickr.com/photos/biscuitsmlp/2247299538 CC-BY-SA

http://www.flickr.com/photos/tammra/283690669/

Because every time a permanent job is advertised...

http://www.flickr.com/photos/t3rmin4t0r/3947963283 CC-BY

The one with the most Nature papers

gets to mate...

We optimise for...

http://www.flickr.com/photos/klausnahr/4437823757 CC-BY-SA

http://www.flickr.com/photos/frozenchipmunk/197591546 CC-BY

Rather than for use and re-use...

...because of the incentives...http://www.flickr.com/photos/daquellamanera/3238300837 CC-BYWednesday, 14 December 11

http://www.flickr.com/photos/lifeontheedge/247473398 CC-BY-SAWednesday, 14 December 11

http://www.flickr.com/photos/turtlemom_nancy CC-BY-SA

We are stuck with “impact”...

http://www.flickr.com/photos/babasteve/3140688308 CC-BYWednesday, 14 December 11

...but we can mould it.

http://www.flickr.com/photos/waltstoneburner/5745387762 CC-BYWednesday, 14 December 11

An assertion.

We want to see research used.

In the right places...

http://www.flickr.com/photos/ol1/6048544977 CC-BY-SA

http://www.flickr.com/photos/velkr0/3472576304 CC-BY

http://www.flickr.com/photos/argonne/3465398655 CC-BY

...at the right time.

http://www.flickr.com/photos/robbie73/3387189144 CC-BY-SAWednesday, 14 December 11

We want research to be re-used and re-usable

Impact = Re-use

Application = Re-use

Commercialised = Re-use

Education = Re-use

Engagement = Re-use

...but also...

Citation = Re-use

http://www.flickr.com/photos/sterlic/4299631538 CC-BY-SA

Can we measure re-use?

Bollen et al., PLoS ONE 4(6): e6022 doi:10.1371/journal.pone.0006022.g002

The web changes everything...

http://www.flickr.com/photos/jurvetson/916142 CC-BYWednesday, 14 December 11

New tracks to followhttp://www.flickr.com/photos/mikebaird/2985066755 CC-BY

ScienceCard by Martin Fenner - http://sciencecard.org/CameronNeylon

Altmetric.com by Euan Adie - http://altmetric.com/interface/explorer.html

Bookmarks = Re-use

Discussion = Re-use

...and we can track them all

http://www.flickr.com/photos/paul_white/5831407787 CC-BY

...on an open network.

But what about...?

Maximise potential...

http://www.flickr.com/photos/pinksherbet/3370498053 CC-BY

...for discovery and re-use...

http://www.flickr.com/photos/pagedooley/3797236989 CC-BYWednesday, 14 December 11

Measure re-use and re-usability...

Optimise for impact

http://www.flickr.com/photos/gsfc/6147894106 CC-BY

...and the easiest way...

http://www.flickr.com/photos/virtualsugar/316200555 CC-BYWednesday, 14 December 11

Not the only way.

...but the easiest and most common

http://www.flickr.com/photos/ehamiter/4607728796 CC-BY-SA

The solutions won’t come from where we expect...

Open networks scale

...enable solutions to discover problems...

...at all levelshttp://www.flickr.com/photos/37850028@N05/5111113034 CC-BY

..from the research

...to the technology...

...to the architecture

http://www.flickr.com/photos/yakobusan/2436481628 CC-BYWednesday, 14 December 11

Build open networks...

Enable discovery...

http://www.flickr.com/photos/pagedooley/2836337974 CC-BY

The rest will follow...

I want to publish more and read less

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